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Picard, Worf, and Dr. Crusher are reassigned from the Enterprise to a secret mission. Meanwhile, the Enterprise is under the command of Captain Edward Jellico, who immediately starts making changes, much to the dismay of the crew.

Nechayev beams aboard the Enterprise and unceremoniously greets CaptainPicard. In her no-nonsense fashion, she informs Picard In his ready room that she is here to relieve him of command of the Enterprise.

Nechayev meets with CommanderRiker, Lieutenant CommanderData, and CounselorTroi in the observation lounge and briefs them that the Cardassians have mobilized three divisions of ground troops (having withdrawn the bulk of their forces from the Bajoran sector) and that their subspace transmissions have increased by 50%. The admiral hopes that the Cardassians are not willing to risk an incursion and possibly war over one system. When Riker asks about Picard, Necheyev tells him that he is to be replaced by one Captain Edward Jellico, commanding officer of the Cairo. Also that their chief medical officer, Dr.Crusher and Security chief, LieutenantWorf, are also being reassigned to a mission. The change of command will occur at 1300 hours.

Since Jellico was instrumental in negotiating the original peace treaty with the Cardassians, Nechayev feels he is uniquely qualified to negotiate with them again. Once Data and Troi leave the observation lounge, Riker reminds the admiral that Jellico can negotiate with the Cardassians without taking command of the Enterprise. She tells Riker that she wants someone on the bridge who has significant experience with the Cardassians, and that's not him.

Picard, Worf, and Crusher are training for their secret mission in the holodeck. They are running a program in a series of dark caves including exercises such as escaping Cardassians, setting mobile shield emitters, and other surprises they might run into on the mission. They take turns and try to best each other's times.

Riker and Jellico in the transporter room

Riker meets Captain Jellico in the transporter room. Riker is immediately overwhelmed by his new commanding officer. Admiring the beauty and prestige of the Galaxy-class starship, Jellico surmises that must be why Riker has never accepted his own command. During the short walk to the turbolift, Jellico lists a series of orders including changing the duty shift rotation from three watches to four by 1400 hours and meeting with the department heads at 1500 hours. They arrive at the turbolift, and Jellico asks Riker whether he prefers "Will" or "William." Riker indicates the former, and Jellico asks where his quarters are. Before Riker can finish his reply, Jellico states the deck number for that room. He departs in the turbolift, leaving Riker befuddled.

Picard relinquishes command to Jellico

A ceremony for the Change of Command of the Enterprise is held in Ten Forward. The two captains are in full dress uniforms while the rest of the crew are in standard uniforms (except Troi, who wears her grey unitard). Captain Picard reads the transfer orders from Admiral Nechayev and instructs the computer to transfer all command codes to Captain Jellico. The Enterprise is now Jellico's.

Riker meets up with Lieutenant CommanderGeordi La Forge, and the engineer asks Riker how long he thinks this change of command is going to last. Riker tells him that they usually do not perform this ceremony if it is just going to be a temporary assignment. Meanwhile, Troi spots the exhausted Dr. Crusher sitting in a corner and goes over to her. Troi asks her if she is sore. They exchange glances, and the doctor says that she wishes she could talk about the mission but cannot.

Picard and Jellico discuss very specific issues on the ship's systems. Jellico says that he can handle anything that comes his way. They then discuss the specifics of Picard's mission in a somewhat coded fashion. Picard reveals that he wishes he had more current information than the two-year old intelligence reports. Jellico offers to send a Class-5 probe later, and Picard happily accepts.

Jellico calls for Riker and passes the order to launch the probe during delta shift. Riker informs his new commanding officer that the new crew rotation is not yet ready and that the department heads believe it will put too much pressure on their personnel. Jellico orders the new duty roster to be ready immediately and dismisses his first officer. Riker leaves, and Jellico makes his dissatisfaction with Riker clear to Picard, who defends his former first officer.

"Captain's log, Stardate 46358.2: The Enterprise is on course for a rendezvous with the Cardassian ship Reklar. Fortunately, I still have time to prepare the ship and crew for the task ahead."

Some time later on the bridge, Jellico, Riker, Data and Garvey stand over the tactical station. Jellico orders several modifications to the terminal and then proceeds to order changes to Science I and II making them Damage Control and Weapons Status. He then orders one battle drill for each of the four shifts. He wants Riker to "get it done" by seeing to it personally. Before leaving on the turbolift with Data, he tells Riker he wants "that fish" out of the ready room.

In engineering, Jellico tells La Forge to overhaul the warp coils, as he finds their performance unsatisfactory. The chief engineer insists that what Jellico is asking will take more than the two days that the captain is giving him. Data, apparently the only crew member with whom Jellico is impressed, calculates that the required actions are possible in the time requested. La Forge agrees but only if the entire engineering staff works around the clock for the two days. Jellico responds with his signature line, "Get it done."

Jellico redecorates

Meanwhile, Jellico is redecorating his ready room, sans fish. Troi enters, and Jellico shows her a drawing from his son of what he believes to be an elephant. Troi tries to explain the feelings of the crew to him. While recognizing that he and the crew are still getting used to each other, it is clear that Jellico does not feel there is any time for a period of adjustment. He orders Troi to do what she can to have the crew accept the situation. She turns to leave, and Jellico informs her that he likes "a certain formality on the bridge" and would prefer that she wears a standard uniform while on duty.

La Forge visits Riker in a corridor and complains. La Forge wants to know how he is expected to get his work done with such a heavy load and with one-third of his staff being reassigned to security. Riker makes it clear to La Forge that Jellico will not listen to him or any of the other department heads. La Forge suggests he try to get Captain Picard, who has not left for his mission yet, to help in persuading Jellico to ease up a little. Riker heeds the engineer's advice and leaves to visit Picard.

Picard practically stumbles into his quarters, exhausted from the training. He admits to Riker that he has not been this tired since he was training for the Academy Marathon. Riker does not want to bother him and leaves without asking his favor.

Picard meets with Captain Jellico in the ready room, and they discuss the mission briefly. Riker calls and informs Jellico that the shuttle is ready for launch. Jellico asks whether he launched the probe as requested. Riker tells him that he has but that he did not know he was supposed to inform his captain about the launch.

After the channel closes, Jellico again expresses his disappointment with Riker to Picard and that he sees why Riker is still only a first officer. Picard reminds the other captain that Riker has been offered command several times and that he will find him a very capable officer if given the chance. Jellico tells Picard that he does not have time to do that for Will Riker or anyone else. Jellico reminds Picard that he is in command of the Enterprise and that he does not expect Picard to come back from his secret mission into Cardassian territory. He also knows that negotiations with GulLemec will not go too smoothly and that neither side will give up anything very easily. He states the Enterprise is his.

Once the members of the commando mission leave the Enterprise on the shuttlecraftFeynman, Picard informs his team of their mission: a secret investigation of the Cardassian planet Celtris III in search of a research facility for metagenic weapons. Picard studied theta-band carrier waves while on the Stargazer. Worf is there for muscle. Crusher is there to locate and destroy any bio-toxins they may find.

DaiMon Solok on Torman V

In order to secure safe passage into Cardassian territory, they enlist the help of DaiMonSolok on the planet Torman V. Picard makes the proposal to him. Solok is worried because Celtris III is in Cardassian territory, and he then accuses the three of being Federation spies. Crusher then begins to charm Solok and even uses oo-mox to convince him to provide passage discreetly.

"First Officer's log, supplemental: We have rendezvoused with the Cardassian ship Reklar to begin diplomatic talks designed to ease tensions along the border."

Riker tells Captain Jellico that Lemec, commander of the Reklar, was beamed aboard and was escorted to the observation lounge. Jellico then announces that he will be waiting in his ready room, confusing Riker and Troi.

Crusher looks down a very steep cliff on Celtris III

Troi, now wearing a standard uniform, enters the ready room and asks Jellico if there has been a miscommunication. He reveals that this is one of his negotiating tactics. Jellico compares Cardassians to timber wolves in that they possess an instinctive need to establish a dominant position in social situations. He is making Lemec wait in order to gain the dominant position. After the counselor reminds him that sometimes a wolf ends up dead in the fight for dominance, Jellico tells her that the trick is to be the wolf that is left standing in the end.

After arriving on Celtris III, Picard reminds Crusher to set her tricorder in order to keep a precise map of their route. She then starts picking up subspace signals, but cannot get a lock on them. By compressing the detection bandwidth, Picard determines that the source of the signal is five hundred meters east and seven hundred meters below their current location. Lynars, which are Celtran bats, fly by them, and Worf pretends not to be afraid of them.

The team comes to a precipice and needs to descend the rock face to the floor, which is over five hundred meters below. As they prepare their equipment, Worf asks Crusher if she is afraid of heights, and she sarcastically says that she is not. The three of them begin rappelling down the cavern.

Jellico has been keeping Lemec waiting for over an hour. Also, the fact that he brings Riker and Troi with him to the negotiating table infuriates the Cardassian. Jellico tells him that if he cannot negotiate anything other than minutiae, then maybe he is not serious about these talks. Jellico then storms out of the room and onto the bridge.

Jellico discusses tactics

Riker and Troi follow him, and he almost gleefully shares his plan of attack. Jellico tells Riker and Troi to let Lemec stew for a few minutes and then to tell him that Jellico is a loose cannon, but he has agreed to meet again. They are to explain to Lemec that he needs to be more reasonable since Jellico is such an unreasonable man and that he can include no more than two aides. After Jellico walks away, Riker notes that the captain is very sure of himself. Troi reveals that he is in fact not.

On Celtris III, the team has finished rappelling, and they are only three hundred meters away from the installation. Picard leads the way, scanning with his tricorder. They encounter a lava tube that runs for seventy-five meters behind a wall. Worf notes that a phaser set to level 16 should suffice. He then blasts a hole in the wall to reveal the tube.

Lemec introduces his aides

Meanwhile in the Enterprise observation lounge, Lemec introduces Captain Jellico to his aides, GlinnsCorak and Tajor. Jellico, along with Riker and Troi, sit at the other end of the table and Jellico accuses the Cardassians of massing troops in staging areas, assembling strike forces, and pulling ships off their normal patrols. Lemec insists they are merely routine training operations. Jellico proposes sending a few starships into the sector for their own training operations. Lemec is more concerned about the Federation's refusal to vacate systems that are "clearly Cardassian."

Jellico is very agitated because he believes the Cardassians are seeking to get those worlds at the bargaining table that they could not take by force. Troi calms Jellico, and Riker states to Lemec that under the terms of the treaty those worlds are still under negotiation. Lemec reveals that they have reports that a small Federation task force has infiltrated Cardassian territory. He says that this action will likely fail, and if it were to succeed, there would be serious repercussions. Before they recess, Lemec asks Jellico where Picard is and does so in a way that implies that he already knows. Jellico tells him that Picard has been reassigned.

Picard, Crusher, and Worf break into the lab on Celtris III

On Celtris III, the team crawls through the lava tube with Crusher bringing up the rear. The two men get out safely, but the doctor is covered by rubble during a cave-in. Worf immediately leaps back into the tube and uncovers Crusher. Shaken but unhurt, they move on. They find a maintenance hatch with three proximity sensors around it. Worf sets up sensor echoes so that they can make it through without being detected. The hatch is magnetically sealed, but Worf is able to bypass it.

They go through the hatch to find a room with only a single device, which has been emitting the theta-band waves. There is no lab. It has been a trap all along.

Cardassians suddenly attack Picard and the others. The Federation team responds with phaser fire and hand-to-hand combat. Worf blocks the closing hatch so that the others can escape, but Picard is still fighting. Worf is shot, and he falls outside the room while the hatch closes. Picard is captured by four Cardassians and reluctantly drops his weapon. Crusher and Worf realize that they cannot help the captain, and they quickly make their escape.

Gul Madred on Celtris III

Back on the Enterprise, Riker notifies Jellico that there are a lot of coded messages from Celtris III. Also, there had been theta-band emissions until a few minutes ago. Jellico orders Riker to get Admiral Nechayev on a priority 2 channel. He tells her the mission was apparently successful since the theta-band emissions have stopped. She asks Jellico if there has been any word from "our friends," but there has not been.

In a stark, imposing room, an unknown Cardassian, who is later revealed as Gul Madred, tells Picard that he is the most interesting challenge to walk through his door in years. He cites Picard's name, Starfleet serial number, parents' names, and place of birth. Then he states that he knows of Picard's extensive experience with theta-band carrier waves while captain of the Stargazer. He reveals that this information was used to lure Picard. Picard asks why he was chosen. Madred responds by telling Picard that he is not allowed to ask questions. Only Madred will ask them, and if he is not satisfied with the captain's responses, then Picard will die.

"May I present Captain Jean-Luc Picard."
"Admiral, welcome on board."
"Thank you. That'll be all, commander."
"Can I get you some coffee, tea..."
"Thank you, no captain. I'm afraid there's no time for the usual pleasantries. I'm here to relieve you of command of the Enterprise."

- Riker introduces Picard to Nechayev who then promptly strips him of his captaincy of the Enterprise

"I wonder how permanent this is gonna be."
"I don't know. They don't usually go through the ceremony if it's just a temporary assignment."

- La Forge and Riker after Jellico becomes captain of the Enterprise-D

"He was your first officer for five years..."
"One of the finest officers that I have ever served with."
"Of course he is, Jean-Luc. I'm sure it'll all work out..."

The episode was originally intended to be a single episode, with Picard rescued at the end of the hour. Michael Piller suggested to split the story into two parts primarily for financial rather than dramatic reasons. Jeri Taylor recalled, "We were in budget trouble and Michael said, 'You know, I think what we could do is make this a two-parter. Have Picard captured and then make it an episode about his relationship with his torturer that takes place in one room. It's a fascinating two-person play and we'll get another episode out of it that way and we'll save a lot of money that will bring us even with the budget.'" (Captains' Logs: The Unauthorized Complete Trek Voyages)

The producers attempted to establish Jellico as more of a "by-the-book" captain than Picard by means of various subtle details. His entry onto the bridge is announced ("Captain on the bridge!"); he himself announces Picard's return at the end of the next episode. He also insists upon crewmembers appearing in full standard uniform when on duty, and has Data wear a command division red uniform when promoting him temporarily to first officer in Part II. His catchphrase "Get it done" when issuing orders was intended to be a counterpart to Picard's somewhat friendlier "Make it so." He also was a family man; after ordering Livingston's tank removed from the ready room, he puts up pictures drawn by his son. The writers wished to stress that Jellico wasn't at all ineffective as a captain despite his run-ins with Riker, his approach was just more direct than Picard's. (Star Trek: The Next Generation Companion)

Rene Echevarria elaborated on the planned TNG/DS9 crossover thusly: " We were going to go to DS9 and that's how we were going to get to the planet in the show. The Enterprise was going to come to DS9 and get a ship. The scene with the Ferengi was written for Quark and I don't think Ron [Moore] changed a word except the guys name. We were going to borrow one of their runabouts which Jellico was going to ask for, but it just didn't work out. Rick [Berman] wanted to wait a little longer before doing a crossover. Actually, it was less expensive, because if you go to Deep Space 9 you have to use at least one of their regulars". (Captains' Logs: The Unauthorized Complete Trek Voyages, page 267)

McFadden between takes

According to Ronny Cox, the removal of Livingston from the ready room had a larger motive. Patrick Stewart hated Livingston's presence in the ready room, and constantly petitioned the producers to remove the fish. Stewart felt that it was inappropriate to have a captive animal in a series that valued the dignity of different species. Cox stated that the producers' decision to temporarily remove was thus a "sort of bone they threw to Patrick". [1]

Troi began wearing a standard Starfleet uniform in this episode when ordered to do so by Jellico; she had not done so since "Encounter at Farpoint" with the exception of the fantasy universe portrayed in "Future Imperfect". This was a costume experiment that Ronald D. Moore had wanted to try and Marina Sirtis was eager to oblige. (Star Trek: The Next Generation Companion) Ronny Cox noted, "I think there were a lot of things that [Jellico] did that were really important for that show. Having Troi put on a damn uniform? Give me a break! This is an officer on a ship and she's running around with her boobs hanging out?" [2] Troi continued to appear in uniform while on duty for nearly all of the rest of the series.

In 2012, Michael Dorn related a story about the production of this episode to the cast of The Next Generation at the Calgary Expo. During shooting while he, Patrick Stewart and Gates McFadden were working in the tunnels of the set for Celtris III at Paramount Stage 16, Dorn and Stewart started laughing uncontrollably. There were many stray cats roaming around Paramount Pictures and as the set was covered with sand, they frequently used it for cat litter. Dorn asked Stewart what he was laughing about and he said, "I don't know how I got here. I was at a seminar at Santa Barbara, the next thing I know, I'm crawling around in cat shit!" [3]

This episode marks the first appearance of the iconic style of Cardassian military uniform seen throughout DS9. In fact, the uniforms made their first appearance in "Emissary", which was filmed before "Chain of Command", but the audience could see them for the first time here.

During the entire time she is on board the Enterprise-D, Admiral Nechayev is not shown wearing a combadge, but once she is back in her office and contacted via subspace radio by Jellico, she is wearing one.

Although the shuttle that Picard, Crusher, and Worf use is a Type-7 shuttle, the set used for the interior is that of a Type-6 shuttle.